Biotechnology Regulatory Services 

Stakeholder Meeting 

December 9, 2020
Welcome

Doug McKalip

Senior Advisor 

Biotechnology Regulatory Services

Animal and Plant Health Inspection Services

December 9, 2020
New BRS Staff

Ibrahim Shaqir

Associate Deputy Administrator

Biotechnology Regulatory Services

Animal and Plant Health Inspection Service

December 9, 2020

BRS Organizational Structure

 Two Programs

• Biotechnology Risk Analysis Programs (BRAP)

– Plants Branch, Plant Pests

– Protectants Branch

– Plant Evaluation Branch 

• Regulatory Operations Programs (ROP)

– Eastern Compliance Assurance Branch (ECAB)

– Compliance Evaluation and Enforcement Branch (CEEB)

– Western Compliance Assurance Branch (WCAB)

 Four Support Service Groups and Science Advisors in the 

Office of the Deputy Administrator

• Communications

• Intergovernmental Operations

• Policy, Program, and International Collaboration (PPIC)

• Resource Management Services (RMS)
BRAP

• Addresses potential plant pest risk and environmental 

impacts of organisms developed using genetic 

engineering on the human environment by conducting 

risk assessments and environmental assessments of 

these products. 

• Reviews permit and notifications applications, petitions 

for deregulation, confirmation requests, potential 

noncompliance with permit conditions, and proposed 

regulatory changes. 
BRAP

Suma Chakravarthy, Branch Chief Biological Scientist 

Srinivasa Chaluvadi

Tyler Reid, 1890 Scholar Rebecca Fletcher

Herbert Eichenseer

Senior Biological Scientist Natalie Howe

Michael Stulberg Ordom Huot

Martha Malapi-Wight Colin Murphree

Sarah Prewitt

Katharine Swoboda-Bhattarai
ROP

• Ensures compliance with APHIS regulations (7 CFR part 

340) through compliance inspections and evaluating and 

responding to noncompliance incidents

• Oversees reports submitted in connection with 

notifications and permits

Doug Grant, ROP Director

Heather Brown, CEEB Senior Compliance Specialist

Elizabeth Burns, Regulatory Analyst
Communications 

• Develops and coordinates BRS communication strategies 

and outreach efforts

• Manages the BRS website content, supports strategic 

and operational planning

• Manages BRS response to Freedom of Information Act 

(FOIA) requests and provides associated guidance

Hannah Hamilton, Branch Chief
PPIC

• Conducts legal and policy analysis; guides policy 

development; manages a compliance assistance 

program; and assists program units to implement quality 

management principle and practices

• Point of contact for BRS international issues, training, 

and program activities and collaborates across the U.S. 

government to support plant health protection and 

trade missions

Kayla Knilans, Biological Scientist

Russell Duncan, Agriculture Science Officer, International 

Services
RMS

• Responsible for all administrative functions as they 

pertain to human, physical capital, and resource 

management; financial management; and data 

management 

• Provides guidance and support on travel, training, and 

employee development

Djene Sylla, Program Assistant

Jason Chatman, Management Analyst

Overview of FY20 Activities;

Look Ahead to FY21 Priorities

Bernadette Juarez

Deputy Administrator 

Biotechnology Regulatory Services

Animal and Plant Health Inspection Service

December 9, 2020
SECURE Rule Implementation 

• BRS by the Numbers

https://www.aphis.usda.gov/brs/pdf/brs-numbers.pdf

• About the SECURE Rule 

https://www.aphis.usda.gov/aphis/ourfocus/biotechnology/biotech-rule

-revision

• Confirmation Request Process 

https://www.aphis.usda.gov/aphis/ourfocus/biotechnology/permitsnotifications-petitions/confirmations/confirmation-process

• Retired the “Am I Regulated?” Process

https://www.aphis.usda.gov/aphis/ourfocus/biotechnology/am-i- regulated/regulated_article_letters_of_inquiry/regulated_article_letters_of

_inquiry
SECURE Rule Implementation 

• Plant-Trait-Mechanism of Action (MOA) Table 

https://www.aphis.usda.gov/aphis/ourfocus/biotechnology/permitsnotifications-petitions/confirmations/plant-trait-moa

• Guidance for Preparing Proposals for Plants with 

Additional Modifications that Qualify for Exemption

• Guidance for Requesting a Regulatory Status Review

• Guidance for Submitting Permit Applications
SECURE Rule Implementation 

International Outreach 

• Publicized SECURE Rule through 98 offices of the Foreign 

Agricultural Service and APHIS’ 28 international offices

• Multilateral, bilateral and regional meetings to share and 

encourage science-based approaches that are proportionate to 

the level of risk

• Canada, Mexico, Brazil, Brazilian Regulators, Latin American and 

Caribbean Countries, Taipei, Taiwan, Korea, Dubai, and Japan

• Upcoming interactions: Korea, EU Delegations; Spain, Portugal, and 

planned Latin American Regional outreach
Petition Pipeline

• Determinations of nonregulated status to date: 133

• Determinations of Nonregulated status in FY2021: (0)

• Determinations of Nonregulated status in FY2020: (1)

• Simplot Z6 Potato (Extension) 08/28/2020

• Draft PPRA + draft EA or extension + draft PPRSA

• Closed comment period (3): Monsanto Lygus cotton; Westhoff petunia; 

Pioneer enhanced yield maize

• Open comment period (1): Pioneer SPTA maize

• Petitions

• Closed comment period (4): Agrivida phytase maize; SUNY ESF blight 

tolerant chestnut; Bayer stacked herbicide resistant maize; BASF nematode 

protected soybean

• Open comment period (1): Pioneer insect and herbicide resistant maize
Other Updates

• Advanced Notice of Proposed Rulemaking

• Regulation of the Movement of Animals 

Modified or Produced by Genetic Engineering

• Oversight of “amenable species” (cattle, sheep, 

goats, swine, horses, mules, or other equines, 

catfish, and poultry) developed using genetic 

engineering intended for agricultural purposes 
Thank You

Bernadette Juarez

bernadette.r.juarez@usda.gov

(301) 957-0934
Overview of SECURE Rule 

Guidance Documents

Alan Pearson

Assistant Deputy Administrator

Biotechnology Regulatory Services

Animal and Plant Health Inspection Service

December 9, 2020
Guidance for Preparing Proposals to 

Exempt Plants with Additional 

Modifications from Regulation
Required Information

 Requestor’s name and contact information, including email

 Clear description of the additional genetic modification(s) that a 

plant or plants can contain and qualify for exemption, e.g., 

• A specified number of changes achievable in cultivated plants

• A specified number of changes achievable in a particular plant 

species

• A type of modification other than those already listed in 7 CFR 

§§ 340.1(b)(1-3).

 A statement of the factual grounds demonstrating that plants 

containing the proposed genetic modification(s) could be 

achieved in conventional breeding 

 Supportive scientific literature or publicly available information 

 Any unfavorable information known to the requestor
Decision Standard

“Could be achieved through conventional 

breeding” means that the genetic modification is 

practically achievable through conventional 

breeding methods in the plant

For example, evidence that multiple desired traits 

or genetic modifications can be introduced in a 

plant on a practical basis would meet this standard
Process

 Submit proposals electronically via 

(b)(4)exemptionrequests@usda.gov

 If there is insufficient publicly available information supporting 

the proposal or APHIS disagrees that plants containing the 

modification(s) could be achieved through conventional breeding 

methods, APHIS will return the proposal and provide the reasons 

for the return in writing

 If APHIS determines that plants containing the modification(s) 

could be achieved through conventional breeding methods, it will 

publish the proposal and supporting information in the Federal 

Register for public comment. After review, APHIS will publish a subsequent notice in the Federal Register announcing its final determination

 APHIS will complete its review and make a final determination 

within 12 months of receiving all required information, except in 

circumstances that could not reasonably have been anticipated

 We recommend discussing your proposal with us prior to your 

first submission
Examples

The Guidance will include examples of proposals 

based on modifications already listed in 

7 CFR §§ 340.1(b)(1-3) 
Guidance for Requesting a Regulatory 

Status Review
Regulatory Status Review (RSR)

If a plant does not meet a regulatory exemption, the 

developer may seek a RSR for a plant developed using 

genetic engineering to determine whether it is regulated.

RSR evaluates the plant pest risk posed by the plant 

relative to that posed by its comparator plant based on:

• the biological properties of the plant;

• the trait (or new characteristic); and

• the mechanism of action (MOA, or how the modification 

caused the new trait to occur).
RSR - Definitions

Comparator plant. A plant used as a comparison or reference for a plant developed using genetic engineering to determine if the 

plant being evaluated poses an increased plant pest risk. 

Trait. An observable (able to be seen or otherwise identified) characteristic of an organism. (§ 340.3)

Mechanism of Action (MOA). The biochemical process(es) through which genetic material determines a trait. (§ 340.3)

Plant pest risk. The potential for direct or indirect injury to, damage to, or disease in any plant or plant product resulting 

from introducing or disseminating a plant pest, or the potential 

for exacerbating the impact of a plant pest. (§ 340.3)
RSR Process – Step 1

 Evaluates the characteristics of the plant relative to an 

appropriate comparator plant to identify whether a plausible 

pathway to increased plant pest risk exists.

 Is there a scientifically plausible hypothesis by which the trait 

and mechanism-of-action could change any of the following 

factors in a way that could lead to increased plant pest risk:

• The distribution, density, or development of the plant and its 

sexually compatible relatives; 

• The production, creation, or enhancement of a plant pest or a 

reservoir for a plant pest; 

• Harm to non-target organisms beneficial to agriculture; and/or

• The weedy impacts of the plant and its sexually compatible 

relatives.
RSR Process – Step 1

 Generally completed within 180 days from receipt of a 

request that meets the information requirements

• If APHIS does not identify a plausible pathway to increased 

plant pest risk, the plant is not subject to the regulations

- APHIS will post the plant, trait, and MOA on its website

• If APHIS does identify a plausible pathway to increased plant 

pest risk, it will provide feedback about the identified 

pathway(s) and the type(s) of additional information, if any, it 

would need to complete a plant pest risk assessment (PPRA). 

The requestor may:

– elect to take no further action

– obtain a permit to allow movement and/or confined release

– submit a formal request that APHIS complete a PPRA

– pause the RSR process
RSR Process – Step 2

 Plant Pest Risk Assessment (PPRA) evaluates the identified 

pathways and factors of concern to determine the likelihood 

and consequence of the plausible increased plant pest risk

• Preliminary finding of unlikely to increase plant pest risk published in 

the Federal Register

• Solicit and review comments from the public

• If APHIS finds the plant is unlikely to pose an increased plant pest risk, 

the plant is not subject to the regulations

• If APHIS does not make such a finding, the plant will remain regulated

 Generally completed within 15 months of receiving a 

complete initial request

• Includes 30-day completeness review for any requested data

• Excludes any pauses in the process

 Anyone can request a re-review based upon scientifically valid 

evidence relating to plant pest risk
Pausing the RSR Process

 APHIS will pause the RSR process after Step 1 until 

receiving a response from the requestor

 APHIS will pause the process while awaiting a response 

to completeness review in Step 2 

 APHIS will otherwise not pause the RSR process after a 

complete request is submitted 

 A requestor can request a pause in the RSR process at 

any time, e.g., if data from a laboratory or field study is 

needed to inform a PPRA, the RSR process can be 

paused until the data is provided to APHIS
RSR Request - Required Information

 Requestor’s name, organization, and contact 

information, including email

 CBI Statement and, if there are CBI claims, CBI 

justification

 Scientific name of the comparator plant

 Genotype of the modified plant, including a 

detailed description of the differences in genotype 

between the modified and unmodified plant

 Detailed description of the new trait
Required Information: Genotype

If genetic material is inserted

 The DNA sequence of the inserted material 

 Annotation of the inserted material, including for each 

construct component

– Nucleotide position

– Name (e.g., 35S promoter, catalase, nos terminator, noncoding 

spacer) 

– Donor organism(s) or source

– Short description of the function, e.g.,

o Enzyme involved in amylose synthesis

o Confers glufosinate resistance

o Native promoter

o Nopaline synthase terminator
If genetic material is inserted

• Publicly available sequence identification, protein 

accession number, and enzyme commission number

• Identify promoters as constitutive, inducible, 

developmental, or tissue specific

– If developmental/tissue specific, describe the stage(s)/tissue(s) 

in which the promotor is intended to be active

• Identify the nature and purpose (e.g., codon 

optimization, change in binding site of an enzyme) of 

any sequence alterations and alignment with the 

unmodified in the donor organism

Required Information: Genotype
Required Information: Genotype

If genetic material is not inserted 

• Identify the gene(s) or genomic region(s) and the 

function(s) that are being modified

• Provide the DNA sequence of the entire modified 

region, including alignment with the unmodified 

sequence
Required Information: 

Description of the New Trait 

 Purpose and intended phenotype of the new trait, 

including any expected differences from the 

phenotype of the comparator

 Available information on the MOA by which the 

intended trait is conferred, i.e., the biochemical 

process by which the genetic modification leads to 

the desired trait or phenotype

 Any expected changes in metabolism, physiology, 

and development due to the trait/genetic 

modification, to the extent known
Description of the New Trait: 

Examples

Trait: Herbicide resistance 

Phenotype: Resistance to glyphosate

MOA: An insensitive form of EPSPS (5-enolpyruvylshikimate3-phosphate synthase) with a decreased binding 

affinity for glyphosate

Trait: Altered tuber amino acid profile

Phenotype: Reduced asparagine

MOA: Potato tuber-specific dsRNA-mediated degradation of 

Asn1 (asparagine synthetase-1) transcripts decreases 

Asn1 protein, resulting in reduced conversion of 

glutamine to asparagine in tubers.
Optional Information

Additional information may be submitted, but should 

be limited to that which informs an initial evaluation

Examples

• Whether the MOA is identical or similar to a previously 

reviewed MOA (provide explanation of similarity)

• Additional information on how the genetic material or 

its product participates in or interacts with metabolic, 

physiological, or developmental processes in the plant 

or in other organisms 
PPRA: Additional Information

Additional information pertaining to the PPRA will not be 

reviewed unless a plausible pathway to plant pest risk is 

identified, and should not be submitted until the requestor 

directs BRS to conduct a PPRA

Thereafter, a requestor can submit additional supporting data 

anytime before APHIS makes its determination

Data submissions should address the plausible pathways to 

increased plant pest risk identified in the initial review

APHIS will use publicly available information and any additional 

information that the requestor chooses to submit when 

conducting a PPRA

FY 2020 Compliance Activities 

and APHIS eFile Updates

Douglas Grant

Director, Regulatory Operations Programs

Biotechnology Regulatory Services

Animal and Plant Health Inspection Service

December 9, 2020
Inspection Selection and Execution

 Compile Post-Planting Report (PPR) data 

• Used to select planted sites (plantings) for inspection 

• Database and GIS

• Consider compliance history

• Lower risk trials selected at lower frequency

 Shift to virtual inspections during pandemic

• Piloted virtual inspections in FY18 (as Monitoring and 

Evaluation Interviews (MEIs))

• 100% virtual inspections beginning in March 2020

• Pre-review records and photos 

• Video conferencing technology for remote visualization

• Remote sensing for trial sites review 43
APHIS GIS Portal and 

Use of Remote Sensing

 Analyze geospatial data gathered from 

applicants and inspections

• Map GPS coordinates 

 APHIS-wide mapping capabilities within a 

data-secure cloud space 

• FedRAMP authorized 

 Remote Sensing 

• Satellite imagery to find best image dates 

to support compliance inspections

• Support or refute observations from 

virtual inspections
Inspection Execution and Compliance

 Compliance Rates:

• FY 19 – 97%

• FY 20 – 95%

 Notices sent in FY 20:

• Compliant Inspections: 80%

• Non-compliant Inspections: 5%

• Other Inspections: 15% 

 Common Compliance Challenges in FY 20:

• Release in areas or quantities not authorized: 12

• Failure to comply with Supplemental Permit Conditions: 19

• Late or missing Post-Planting Report (PPR): 28

• Late or missing Field Test Report (FTR): 21

• Often associated with pandemic related challenges 45
46

FY 20 Unique Locations Planted

Total 1,027

92
FY 20 Conducted Inspections

47

51

Total 544
% of Inspections 

Conducted By 

Organization

FY 14-20 (Even 

Years) 

FY BRS PPQ State

14 6.6% 85.4% 8.0%

16 56.2% 36.8% 7.0%

18 69.1% 23.7% 7.2%

20 95.6% 3.9% 0.5%
FY 20 BRS 

Inspections 

by Quarter 

Quarter New Cumulative

1 69 69

2 89 158

3 69 227

4 317 544
APHIS eFile Update

and

ePermits Transition
APHIS eFile Progress

Improved User Registration and continued 

development throughout BRS’ Pilot Program!

48 Pilot Applicants 82 Authorizations 

Submitted

59 Authorizations

Processed
Transition to APHIS eFile

APRIL 1, 2021

APRIL 4, 2021

APRIL 5, 2021

 Last day to submit notifications in APHIS eFile

 Last day to submit any permit and notifications 

applications in ePermits (includes XML applications)

 Applicants must use APHIS eFile to submit permit 

applications

 Applicants can use APHIS eFile to request confirmation 

of exemption from regulation
 Supportive user guides 

 Instructor-led and recorded training for applicants:

• Navigating the Applicant Portal

• Using BRS’ updated Permitting Assistant

• Preparing and managing Permit Applications

• Submitting requests for confirmation of exemption 

from regulation 

 Update on BRS website 

• Sign up for stakeholder registry at: 

https://www.aphis.usda.gov/aphis/ourfocus/biotechnol

ogy

Transition to APHIS eFile
ePermits Future Availability

 Applications submitted in ePermits will complete 

their life cycle in ePermits

 Compliance reports for ePermits authorizations 

should be submitted in ePermits

 For the foreseeable future:

• No restrictions to ePermits read access

• No data migration from ePermits to APHIS eFile
APHIS eFile Early Adoption

 Get acquainted with the user interface

 Submit multiyear permit applications

 Take advantage of “Previously Submitted 

Constructs”

 Set up sharing accounts for their teams

 Visit https://efile.aphis.usda.gov/

• Register with your eAuthentication Account

• Submit your first application!
Contact APHIS-BRS eFile Team

Thank you!

efile.communications@usda.gov

Questions?

Comments?

Need help?

Want to transition early?
Closing

Doug McKalip

Senior Advisor 

Biotechnology Regulatory Services

Animal and Plant Health Inspection Services

December 9, 2020